The biggest flaw, IMO, is the character of Count Fenring.
He's built up over the course of the book as an invincible killer, the ace in the hole. And then when ordered to kill Paul he doesn't... because eh, he doesn't wanna.
I just finished Dune and Dune Messiah. I'm starting Children of Dune which a lot of people say is the best one. Also if anyone else is thinking of jumping on the Dune wagon, I recommend the leather bound Barnes and Noble edition.
Yeah, Children was my favourite in the series. Followed by God Emperor, which I thought was the worst in the series. But Chapterhouse was a solid ending, probably my 3rd-best in the series. But yeah - I loved Children.
The first several Dune books and the Dune encyclopedia are easily the best of Dune. Herbert still had wild ideas in the last few books, but they had long ago ceased to be interesting.
The stuff his son and the other guy hacked out are awful. It's bad science fiction schlock, well below par, and then made even worse by it being built off the corpse of something that had value and some talent behind it in it's day.